@darkmonk: Well the new engine wont use text content, but rather position on page to detect headers and footers. And I will probably remove the current remove header/footer option and replace it with a generic "remove content" option.

It might be a good idea to keep it. Just re-define it as remove content since it can actually match any text in the document. This could be helpful for poor PDF conversion for instance where the headers and footers are interspersed in the middle of the text in say Mobi or Epub files.